An Evil beginning
by TheOffRoad42
Summary: Ash and his friend stop by an inn to go to sleep, but soon after they are kidnapped by an Evil organization planned on using ash to rule the Pokemon world. Rated T for violence and mild language.
1. Chapter 1: A Normal Day

This story begins following our traveler, Ash Kectum, and his friends, Serena, Clemont, and Bonnie. It was about dark around 8 or 9 o'clock. Ash was nearing his finally gym. If he beat this gym, he would be able to move on to the Pokemon league. As our travelers were walking, a couple of a shadows were moving in the bushes, but they weren't team rocket. They are a secret evil team that have plans to kidnap Ash and his friends.

"Ash, are we there yet. I'm bored and what to go to sleep," said Bonnie.

"Don't complain Bonnie, we're almost there," said Clemont, trying to keep his little sister under control.

Clemont was right. As they kept walking, the town came into view. The lights were on, making it easier to see. They all began to run, expect Clemont.

"Guys wait up!" Clemont yelled.

"Last one there is a rotten egg!" Ash yelled.

All of them ran as fast as they could to the town. Ash was the first to get there, Bonnie second, Serena third, and Clemont last. They then all walk into town. Most places were closed because of how late it was. They stopped by an inn. The entrance was nice and roomy.

"Hi, how are you doing today," The clerk asked.

"We want two rooms please," Ash said.

"That will be 1,000 Poke dollars," The clerk replied.

Ash then handed the clerk his money he had earned from his many battles. "Have a nice day," The clerk said, as the friends walked up the stairs to their rooms.

* * *

Three grunts behind a tree are following a group of friends go into a inn. The grunts are wearing gas masks or painters masks. They are all wearing black hoodies.

"So, we wait until the lights go out. Then we climb through the window into the bedrooms. Dan will be waiting outside in the truck. We handcuff the kids and throw them into the back. Got it?"

"Yes sir," The other two replied.

They then waited until the lights in the room were out. They then sneaked their way to the window they would be going through. Once in, one of them threw out a hypno and put the two girls asleep. The other put handcuffs on them. They then pushed them out the window and into the truck. They went to the next room where they did the same thing. The mission was complete. They then drove off, like they weren't even there.

* * *

Ash woke up in handcuffs. He looked around, wondering were he was. He saw his friends laying down by him. He figure out that they were in a cell and someone was walking down towards them.


	2. Chapter 2: The Dungeon

**I own Justin and Alice. Do not take them. (I'm also a new user. Good luck for me)**

* * *

The figure kept walking, it's steps getting louder and louder. Ash's friends started to wake up too. They all looked at the shadow, creeping up to the bars. The now man walked in front of the bars, he had a Pokemon Ash has never seen. It was like wolf, but with rocks sticking out of it's main. The guy petted the Pokemon.

The guy was tall and wore a red hoodie with a symbol on the left shoulder. It showed a gas mask with stick people around it. The guy was also wearing a gas mask. The gas mask had many stickers on it. He had military pants and military boots. He also had something in his pocket yet it didn't look like anything Ash had seen.

"Do you like the dungeon I put you in. Not comfortable but roomy," The guy said, being sarcastic.

Ash then ran up to the Bars. "LET US GO!" He yelled.

The Guy did not listen to him, he then pointed to other three, "You guys don't seem the talking type. Makes sense from your character files we have. The inside people we have helped me figure out how to kidnap you guys. Props to them."

Bonnie, still half asleep, crawls over Clemont.

"Where are we at? Who's that Pokemon? I'm scared." Bonnie then starts to cry.

The guy then sees this. He walks over and then squats down to her level. "It will ok. I have something special for you. You're going to get your own room. You'll get to play with Pokemon. I have that Pokemon you had with you too."

Bonnie cheered up a little, but still was confused.

"You guys have fun, I'm gonna go do some stuff before I pull out of that dump." The guy says before walking away, the Pokemon following him.

* * *

Justin then started to walk away. The plan was going out well. He had them in his grasps. All he needed to do is make them side with him. It wouldn't be easy but he had a machine that could do it in less than 10 minutes. He knew this kid more than the kid knew himself.

His girlfriend then walked up to him, her glare in her eyes reminded him of the time they met. It was a fun time.

"How's the plan going Justin," She asked.

"It's going Alice, you know that, and also are you sure that you will be able to brainwash that little kid?"

"Yes I will able to. Maybe after we should hang out, like old times," Alice said.

"Yeah, like old times," Justin said before walking away and to the machine.

"Is it ready yet? I've been waiting for it to be done by now," Justin questioned.

"It is done leader," The scientists replied.

"I guess it is time to add new recruits to the team," Justin said before giving out a small laugh.

* * *

The friends didn't do much when he was gone. They only just sat around. Some of them even were glad when The Guy came back. The Guy grabbed out his keys and unlocked the door. The group of friends then walked out of the cell.

"It comes to me to be a surprise that none of you asked my name. That is just not good manners. Anyway, my name is Justin. I started out in the Alola region and when I destroyed the Elite four, I create a Evil organization called, The Scavengers. When I heard about you, I came here to Kalos to capture you."

"What are you doing with us? Why do I matter to you?" Ash asked.

"That is a really good question. Let me answer that. All of you stand in a single file line, shoulder to shoulder." The group of friends went into a line formation. Ash first, Clemont second, Bonnie third, and Serena last.

"You see, when Ash started out his journey, he was attacked by spearows, but not to fear, his pikachu was there. It lashed out so much energy, it could've killed someone, but it didn't, for Ash somehow survived the shock. Then a legendary pokemon flew through the sky. After this though, Ash would never be the same. He couldn't die, He couldn't get older. Ash notice after multiple birthdays. He didn't look like he was becoming older, but he took control of it and explored the other regions without care. He could become a pokemon master without no one knowing."

Ash's friends then looked at him. "You were hiding this along?" Serena asked.

"Yeah, but it didn't matter to anyone at the time and it still does."

"But today it does trainer Ash. You see-" Justin then pulls out the weird object from his pocket, "This is a 'gun' and this thing was made before pokemon were a thing around the world. Guns could kill people with one shot, other times, they took more. Sometimes they were bigger, sometimes smaller. I am going to show you that Ash s immortal."

Justin then points the gun at Ash. He then pulls the trigger. It doesn't shoot. "Is it Jammed, or is it?" Justin then points the gun at Clemont. Clemont starts to sweat. _Please be Jammed,_ _Please be Jammed,_ _Please be Jammed,_ Clemont thinks to himself. Justin then pulls the trigger. It goes off and Clemont falls to the ground into a pool of blood.

* * *

 **Stay tuned for chapter 3. I still own Justin and Alice, NO BUTS.**


	3. Chapter 3: Evil begins

**I also forgot to say review this story. I want see your thoughts on the story. I still own the OC so don't take them. Have fun reading.**

* * *

Bonnie was the first to cry. She fell to the ground near him. Next Serena came by her side to comfort her, but she was pushed away. Ash then ran at Justin but was pulled away by his guards.

"Ash, that was rude. You don't get into fights like that," Justin said.

"It was rude to kill Clemont!" Ash replied.

The guards then pulled Clemont's body away. Then more guards took Bonnie away to comfort her with her pokemon.

"Now I'm left with an angry 10 year old kid and a blonde. Never thought I would be in this situation," Justin said before leading them to a weird pod with wires attached to it. The pod was human sized and had class where the head would be.

"Now it is time for you to leave your old self behind and join our organization," Justin said.

It got the two confused and scared of what was going to happen. They both started to sweat in fear. Justin then open the door to the pod.

"Come on Ash, enter into the new world, our world," Justin said.

"No, I don't want to," Ash said with fear.

"Push him in guards," Justin demanded.

Ash was then pushed into the machine. He kept trying to stop them but it didn't work. he said his last goodbyes to Serena and then let it happen. The machine came to life. Light started to flare inside the pod. Serena could hear light screams from the pod. Soon, the light came to a stop and so did the screams. It was presented that Ash had not gave in until the very end. Ash then stepped out of the pod. Serena then became surprised. Ash now had red eyes. He started to smirk.

"So Ash, Do you want to join now. You seem to be better," Justin asked

Ash then looked at Justin, "Not until Serena joins," Ash replies.

"I'm not going to join. Even if that's leaving Ash behind," Serena replied.

The guards then grabbed Serena and threw her into the machine. Ash starts to laugh. The same thing happened as last time. When it was done, Serena walked out. She had red eyes too.

"Now will guys join," Justin asks.

"Yes," They said at the same time.

"Lets get you suited up then."

Justin, Ash, and Serena all walk to the armory which had clothes, Pokeballs and other equipment.

"Girls are on the left and Boys on the right," Justin told them. They then found clothes the liked and went to go put them on. They also got their pokemon back in black and red Pokeballs. New Ash was wearing a black hoodie and a gas mask. He still wore his hat, but now it was red and black and had the scavengers logo on it. He then wore Military pants and boots. New Serena was wearing a red hoodie and a painters mask. She didn't put her hood on so she could show her black and pink hair. She too, wore Military pants and boots. Once they saw each other, they came together and gave the other one a kiss. It was at that moment that Ash and Serena were dating.

"You guys look great, but no time for kissing right now. I need to send on your first mission. Taking over Lumisoe City."

After Justin told Ash and Serena the plan, they were sent off to Lumisoe City in a helicopter. They were dropped off at the top of the Tallest building. Ash grabbed out his now Raichu.

"Raichu use thunder," Ash told his Raichu. Clouds started to form over the city. The clouds were filled lots of energy. Then the first lighting broke the silence. Were it hit caused a fire which was spreading quickly. Then more lighting came from the clouds. Soon there was endless lighting. The entire city was up in flames. Ash and Serena laughing a little. The sat together as they saw the city burn to ashes. They also went in for a kiss.

* * *

Back at the lair, Justin was getting ready to go somewhere. He had already heard that Ash and Serena were successful.

"Be careful Justin. I trust to do that ok," Alice said.

"This is the last thing I need to do before we can take the world by storm," Justin replied.

He then walked off without telling anyone what he was going to do.

* * *

 **So yeah, that's chapter 3 guys. Don't forget to Review because I want your feed back. Also I somewhat want fanart of Evil Ash and Evil Serena, so if you guys can do that and send me, thanks. I will continue writing.**


	4. Chapter 4:A storm is Brewing

**After going over my story, I notice many errors and mishaps. I going to try my best to not mess up. Please also review the story. I want your feedback but I'm not getting it. It makes me sad, but right now, we need to continue the story. Lets read!**

* * *

The trail Justin took was hard and took some time. It was raining and made it hard to see. Many trees blocked the way so he had to move them. It would take him and hour to get to his destination. Once he was there, which was a pool in the middle of a forest, He took out his decidueye to get ready for battle.

"Yveltal, I have long wait to meet you," Justin said.

A dark purple color started to grow in the pool. A pokemon started started to emerge from the pool. It spreaded it's wings open. Justin could feel a dark aura around him, but it only fueled him. Yveltal letted out a battle cry. Justin was the first to move. He bonded with pokemon so much that didn't have to tell the pokemon what to do. He only had to do hand gestures. Decidueye then used leaf blade, which hit yveltal, but yveltal went for a counter attack with a shadow ball. Decidueye dogged the the ball and shot one of his arrows. It missed and yveltal used his special move, Oblivion Wing. It hit Decidueye straight on and fainted him. Yveltal also restored it's health.

"I still got more pokemon," Justin said with a smirk.

Justin then sent out his lycanroc. His lycanroc was the day form, so it was faster than yveltal. Lycanroc went for a stone edge. It was a critical hit and brought down yveltal's health. He looked like was tried, so Justin went for the catch. Justin grabbed out a ultra ball. With a flick of a wrist, the ball went flying at yveltal. It hit yveltal and captured it.

"I was lucky this time, this could've gone way longer," Justin said to himself before petting his lycanroc and going off back to the base. He would now began to help out Ash and Serena on their journey to capture the Kalos region.

* * *

To be fair, team Rocket didn't know what went down, but they do know what happened after. While James and Jessie were wondering what happen to Ash and his friends because they haven't seen him, The news broadcasted the night when Ash and Serena were lashing hell onto Lumisoe city. It got their heads wonder what happened.

"Why would Ash and Serena do it? They were not at all Evil or wanting to do that. And where are the other two?" James asked himself.

"Someone has to be behind this and we have to find out," Jessie told James. "It could competition."

"Lets do it now then. Boss would not like it," Meowth said.

"Should would call Boss, he might help us?" James asked.

"I agree, we should ask Boss," Jessie answered.

They then called Giovanni for help.

"What is it now?" Giovanni asked.

"We think that we have competition Boss. Ash and Serena were spotted at the top of Lumiose city when it was going through a thunder storm that caused major fires and total destroyed the city. We are thinking that a secret evil organization turned Ash and Serena evil, which then caused them to do this."

"Is that so. I send multiple teams out there to deal with the problem. If your righ-, no, this might be it."

Giovanni then pulls up a newspaper from a region called, the alola region.

"It's said here that 'a team of evil people called, The Scavengers, are raiding people's homes and causing chaos in the region. They wear red or black hoodies with gas masks or painters masks. Stay away from them at all costs.' Send me a picture of Ash and Serena."

Jessie then pulls out her computer and sends a picture of Ash and Serena on top of the building.

"They're wearing the same stuff, but why would a gang from a different region want to capture a group of kids and use them as a way to destroy a city. I need you to see if they do anything more before I can send troops. If they do something, follow them when the leave. They might lead you somewhere. I get to you as soon as I can. Over and out."

* * *

Giovanni then goes off to meet with his assistant. She looks at him with a confused face.

"I need planes that will be able carry troops to far away places," Giovanni asks.

"Why, is there something important?" His assistant asks.

"We've got troble and I need to handle it myself."

"Ok, two transport planes are ready to use. See you later Boss."

Giovanni then walked away. Something big was going down.

* * *

Ash and Serena rode back to base in the same helicopter. It was a nice and cozy ride back. Ash and Serena held hands during the trip. Once they got there, they were greeted by Alice, who was waiting for them.

"I'm glad you were able to do it, we will be setting up or teams inside the city to confirm that we have it," Alice said to them.

"Where is Justin? He was here before we left," Serena asked.

"He went off on his own to go do something. He said something like 'it is time to begin the final chapter' or something like that. He'll be back soon. You can wait by going to your quarters and messing around or something else."

"We'll be off then, see you later," Ash said to Alice.

The two then walked off to their own room, which was by Justin's. They messed around, played with each other, told the other jokes. They just had fun. They then heard a knock on the door. Justin walked in to greet them.

"Great job guys, but your work isn't over yet. We still need the rest of the region and I'm going to help. You see, I caught a pokemon called yveltal. At the start of the scavengers, I want to catch yveltal to bring evil across the world, but yveltal was in a different region. I waited until I was big enough and then went off, but then side tracked by catching you."

"So we'll start this tomorrow," Serena asked.

"Yes and we will continue until sun down," Justin replied. "See you guys tomorrow."

* * *

After the conversation, Justin went off to his training grounds. He threw out his new pokemon, yveltal. The pokemon roared with excitement. This was Justin pokemon now, and Justin was able to destroy whatever he wanted. He could destroy anything, ANYTHING.

* * *

 **Looks like a clash is coming in chapter 5(probably). Please review if you want to. I just want feed back, and thats all. I will continue the story if I don't get feedback. Anyway, thank you for reading. See you later!**


	5. Chapter 5: A start to a epic battle

**I'm very sorry for the delay. I have been trying best to get this but I have stuff to do. I'll try to upload daily still but not this time. This will a good chapter and will probably be long. Please review and enjoy.(Please review because I want your thoughts. Even if they are negative)**

* * *

Today was going to be a long day and Ash and Serena knew that. Today they had to go town to town, taking out the police and main buildings, then leaving the rest to the grunts. They would do this all day until they got all of towns or it became brighter outside. Justin said though that they might continue, even if it is day. But before all that, they were going to suit up and train.

"Do we really have train. We are perfectly good right now," Serena said while getting dressed.

"Justin said that we would be watching over the newbies. They need a little touch up he said," Ash replied.

"But that's even worse. I just want to do this now and then hang out with you."

"We can't go now, we have to catch the townspeople off guard so they don't alert other towns that we are raiding them."

Serena then remembered that this was going to be a 'sneak' mission and not a 'go in there, guns blazing' mission.

"I understand," She said.

"Lets get going now, we don't want to miss breakfast," Ash said before running to the cafeteria.

* * *

James was the first to wake up. The sun was shinning, birds were chirping, and today was the day they would be figure out what the heck was Ash and Serena doing and what are their plans with new organization they never knew. James then woke up Jessie and Meowth.

"Time to go see whats going on," James said after repeatedly poking Jessie in the face.

"Stop it. I want to sleep more," She said before dozing off again.

James gave up and went on the Kalos news to see anything new. Most of the stuff was about yesterday, with new stuff. People wearing gas masks take over Lumisoe city. They attacked people that came in their way, but nothing about Ash or Serena. He shut down his computer and went to go to sleep, but before he could lay down, he got a call. He looked at who was calling. It was Giovnnai.

"Have then done anything yet?" Giovnnai asked.

"They haven't done anything but take over Lumisoe city. They have grunts roaming the city," James answered.

"I'm coming right now so please be ready,"

James then put down the phone, and then told Jessie and Meowth.

* * *

Justin was about to head to the cafeteria before remembering that Alice wanted him to Meet her at Bonnie's room.

 _Flashback_

 _Justin was talking with Alice about the plans for tomorrow._

 _"I was planning on sweeping to one city to another at dark, and then letting the grunts do the rest," Justin explained_

 _"I like that plan, but it might trier out Ash and Serena. They're still human beings and not super humans," Alice replied._

 _"Then we gear them up before battle, and then send them off to their mission,"_

 _"That's better, but before we train, I want you to stop by Bonnie's room. I want to show you the progress I've made,"_

 _"I'll come before breakfast, now lets get to bed," Justin and Alice then walked back their room and went to sleep._

 _End of Flashback_

He then walked down the halls to Bonnie's room. Once he got there, Alice was outside the door, waiting for him. She didn't look to happy though.

"Where were you? I've been wait for you for some time," Alice complained.

"I'm sorry, it took some time to get ready. I also almost forgot," Justin explained.

"I'll let you off this time, lets get back what I want to show you,"

They both walked to see the lightly colored room. There was many pictures and toys of pokemon, and the room also had a TV. The TV was showing some sort of cartoon, but Justin didn't recognize it. Bonnie was playing with her pokemon, Dedenne. When they walked in, she didn't get scared or want to cry, she just said hello Mom and Dad.

"Wait, did she just call us 'mom' and 'dad'?" Justin asked Alice

"I brainwashed her so she forgot about her old life and now she thinks that we are her parents. I felt that this was the best way to keep under control," Alice responded.

"So that means that I'm a dad?"

Justin then looked at Bonnie. She smiled back, then went back to playing with her Dedenne. _I was father now,_ Justin thought. Alice then walked over to Bonnie to play with her. Justin then said goodbye to the two of them and went train. He decide to skip breakfast and just eat snack along the way. Now he was doing this for his now Daughter.

* * *

Ash and Serena were walking up and down the lines of grunts to see who was here and who was not. Right now, everyone was here. They then finished roll call and began their speech.

"As part of the Scavengers, We shall fight for the organization and not just ourselves. We shall fight until the end, and we shall have no mercy. It is time for the reign of the Scavengers," Ash said.

The grunts erupted with cheer and began to fill the trucks and vehicles. Ash and Serena would be at the head of the pack in a helicopter. It was 9:00 pm and it was pretty dark so they trailed off to the first city, without knowing that Team rocket was already there.

* * *

Giovnnai and the rest of team Rocket had landed down in Kalos. James, Jessie, and Meowth was there too. They thought that Ash and Serena would definitely would come here first, but they didn't know when. They mostly at night because their last attack took place during night. They setted up camp and fortified the town. It was James's and Jessie's role to watch for anything suspicious.

"I really do not want to do this," James said

"But if we do, we can more recognition," Jessie replied.

"But still, this is a horrible job. We get to be the first to get beaten up," James complained more.

"Wait, I think I see something, no, multiple somethings," Meowth yelled.

He was right, Multiple helicopters and Trucks were coming this way, and they weren't Team Rocket. James ran off to tell Giovanni, but it was to late, and one of the helicopters shot a rocket right at the town.

* * *

 **Don't worry, I'll try to get chapter six out In about 2 days. I have a announcement though. I will beginning a new series off of Splatoon. I didn't want to do it now, I wanted to finished this first. So, sorry for the delay, please review, and have a great day, or a decent one. See you later.**


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